I think that this notion of being progressive is relative.
Was President Hugh B. Brown progressive? He was the most vocal proponent of lifting the priesthood ban in the late 1960s. He was opposed primarily by Elders Joseph Fielding Smith and Harold B. Lee. So while we wouldn't consider President Brown progressive in the context of society as a whole, he was progressive in some ways when compared to Elder Smith and Elder Lee. And when Joseph Fielding Smith became President of the Church, he did not call Elder Brown back to the First Presidency. I think that by comparison, we could say that President Brown was a progressive voice in the Church. I think in the same way, people view Elder Uchtdorf as a progressive voice in the past First Presidency (which had some progressive trends I think, which we could identify if we wanted to). But this does not mean that Elder Uchtdorf is a progressive by any stretch of the imagination outside of that comparison (he wouldn't be progressive by any sort of modern societal view).
I think that it is ignorant to think that the Apostles all share the same sort of world view. This may not create factions so to speak, but it certainly means that there isn't unanimity on every issues. These sorts of disagreement were quite visible in the past, in often public disputes (consider the whole Talmage, Smith, Roberts issue). I think that the loss of the visibility of these disagreements has been helpful in some ways, but also not particularly helpful to the general membership in understanding that diversity in viewpoints is healthy for the Church, and makes a unanimous coming together all that much more significant.

Here is the problem with this idea -
Isaiah 40:28-31
Hast thou not known? hast thou not heard, that the everlasting God, the Lord, the Creator of the ends of the earth, fainteth not, neither is weary? there is no searching of his understanding. He giveth power to the faint; and to them that have no might he increaseth strength. Even the youths shall faint and be weary, and the young men shall utterly fall: But they that wait upon the Lord shall renew their strength; they shall mount up with wings as eagles; they shall run, and not be weary; and they shall walk, and not faint.
Proverbs 3:7-8
Be not wise in thine own eyes: fear the Lord, and depart from evil. It shall be health to thy navel, and marrow to thy bones.
These are allusions to other passages of scripture - and in that context, they are not a health code. The Word of Wisdom is not framed as a health code by these phrases - only by decontextualizing it (of course, that's a relatively common thing in the Church, which has reduced the Word of Wisdom effectively to a handful of thou shalt nots ...)
Of course, this becomes a greater challenge when we both try to interpret it narrowly and very broadly at the same time.

The Word of Wisdom was never a health code. It only became seen (over time) as a health code when it could be defended on that basis. And certainly some aspects of it are healthy (the tobacco issue for example). But we continue to try and defend every part of the policy of the Word of Wisdom as currently implemented as a health code when almost some aspects of it (especially the way in which it is interpreted in policy) simply don't correlate well with health issues.

Robert wrote:
I don't really agree with this although I probably get to the same place. The 1828 dictionary doesn't use the word "transmit" in it's definition of translate. And part of this is because the issue is more about categories. Early LDS had very little interest in definitions of the word "translate," as opposed to the word "author" where they had a much greater interest beginning with the criticisms that came out of the statement of Joseph Smith as author of the Book of Mormon that appeared with the publication of the copyright statement that is published (according to legal requirements) in mid 1829. To answer this, in November of 1829, Oliver Cowdery effectively quotes the 1829 dictionary entry for author in a letter responding to just such a concern. The 1828 dictionary includes this statement as part of that definition:
In that letter, Oliver suggests that Joseph "was the writer of it, and could be no less than the author." This as opposed to Joseph being merely a compiler or translator suggests that while translating was viewed more or less as part of transmission of a text, what Joseph was doing wasn't limited to strictly transmission in his production of the Book of Mormon. Further, what we see in this letter is that translation was viewed in the same category as a compiler. In modern thought, we have, of course, replaced this notion, as we see translation isn't merely a mechanical process but something far more involved in communication, and translators are often given more credit now than there were in the early 19th century for their role in the communicative act that a translation represents that is independent of the original source. In the sense that I disagree, it is precisely in this area where we have some disagreements - that is, I am not sure at all that there was much of a nuanced view of what a "naked translation" was as opposed to some other kind of translation (at least not in popular thought). Translation certainly wasn't conceptually a container for this additional sort of content - it was simply given that extra content by the way in which the notion of translation was categorized (as not normally involving any sort of creative input on the part of the translator). Now, we almost certainly see translators as being more of an author, and we see translators being given a copyright independent of the original author of a text (and even more extreme, perhaps, I am sure you remember the issues with Qimron and Strugnell over the copyright assigned to a reconstruction of MMT in the Dead Sea Scrolls in the 1990s ....).

One of the problems that we face with reading scripture is that we don't engage in any sort of "naked" reading of the text, we always read with - we read with all sorts of things (our knowledge, our assumptions, the cultural and societal baggage, and so on). Nephi, for all of his claims of removing plain and precious things, ends up also removing things from the text for his descendants. He discusses this in some detail in 2 Nephi 25-30. Faced with a recognition that reading Isaiah as the Israelites traditionally read Isaiah didn't actually make the Israelites any more righteous, Nephi replaces that cultural and societal knowledge that he has with a process of "likening" scriptures unto themselves. And Nephi doesn't just explain how this is to be done, he proves examples, where he takes his own prophecy, and then uses the words in Isaiah to interpret his own prophecy - radically altering the meaning of those passages in Isaiah. In a way, reading the Isaiah in the Book of Mormon by trying to understand the Old Testament Isaiah in its own cultural milieu can only result in a failure to understand Isaiah as Nephi intended it to be understood. Only be separating ourselves from that historical and contextual knowledge can we begin to approach Isaiah as Nephi suggests.
What comes out of this is the idea that we define as individuals and groups meta-narratives that determine what scripture means and how it should be read. In some cases, this already costs us "plain and precious truths". Nephi's response to this idea is quite simple - when we read with the Spirit, we gain plain and precious truths to replace whatever is lost (perhaps in Nephi's view, these are equivalent).
Consequently, this sort of question only makes sense if we start by carefully defining what it is we mean by "plain and precious truths", what we mean when we talk about removing them, and so on. If we alter the text, do we lose plain and precious truths? If we cut the Song of Songs, from the Old Testament, would that cost us "plain and precious truths"? If we translate the text from its original language, and we use a theologically motivated interpretation to guide our translation, does that cost us "plain and precious truths"? What if we ignore the historical-critical context, and we liken the scriptures unto ourselves using only the translation that we have in front of us? Does that cost us "plain and precious truths"? I think in the long run there are many ways that we can lose plain and precious truths. But just as often, the notion of plain and precious truth is itself an idea that is narrowly understand and problematic in its own right. Brigham Young suggested that the Book of Mormon was translated for a specific group of people at a specific point in time, and that should it have been translated for others at another time (or even the same group at a later time) it might have been quite different. In the same way, I am not sure that simply excising material is the only way or even the best way to understand this concept.
I think its valuable to understand what Nephi meant when he uses this idea, and to try and understand how his own approach of likening scripture somehow changes the problem (or even offers a solution to it as he seems to be suggesting).

https://en.wikipedia.org/wiki/Prooftext
The challenge we have isn't that we prooftext from time to time. We actually have the idea of prooftexting built into our scripture (and thus into our doctrine, right?). Nephi's likening scripture unto himself is nothing less than prooftexting. The idea that prooftexting is bad is a predominantly protestant idea that comes out of certain ideas about the nature of scripture (that we don't generally hold to). Where it becomes bad for us (as Latter-day Saints) is when we confuse the prooftext and our intention/interpretation based on the prooftext with the intention/interpretation of the original author of scripture. It's okay for Nephi to repurpose Isaiah in the context of his people and their situation. It's not okay for Nephi to then claim that this is really what Isaiah intended all along ....

I think that part of the problem is that we assume that everyone starts in the same place, and ends in the same place. And this simply isn't true.
The Book of Mormon illustrates this problem really well in the narrative in First Nephi that deals with the vision of the Tree of Life. Lehi has this vision. He describes it to his children. And Nephi describes to us two completely different responses. Nephi goes and asks to receive the vision, while Laman and Lemuel argue over what it means based on the description that their father gave them. Not long afterwards, Nephi receives the vision himself, and then finds Laman and Lemuel still arguing about it. Now, Nephi, who has seen the vision can help Laman and Lemuel in a third approach (not as good as the first, and better than the second). But what comes out in Nephi's explanation fascinates me (so much so that I have written about it). Nephi writes this for us:
What happens here? Nephi experiences the vision. Even if the vision that he is shown is completely identical to the vision that his father saw, he can see things that his father doesn't because he pays attention to different aspects of it. At the same time, it seems quite likely that as Nephi's mind was swallowed up looking at the water, that he may have missed other things that his father saw in greater detail than he did. Revelation (at least in the sense that Nephi provides it here) is always a personal experience. It can only be experienced through our own experience (through our own language and understanding, and our own experience of the world that we are in).
There is a certain irony, when we get to this lesson in the lesson manual for Sunday School, because inevitably we are presented with interpretations of the vision. In other words, if we liken the scriptures unto ourselves, we (the class) are treated as Laman and Lemuel, being fed interpretations made by others. In fact, the point of the narrative in the Book of Mormon is not to encourage us to be like Laman and Lemuel, but to become like Nephi, and to witness the vision for ourselves. But we have to understand that even as witness the vision, our experience of that vision (especially now, some two and a half millennia later) could be radically different from the vision that Nephi experienced, and our interpretation or understanding of that vision could be in places quite different from what either Lehi or Nephi understood.
I think, sometimes, we start from a set of assumptions about revelation that turn out to be incorrect or even inappropriate. We like to think that revelation reveals absolutely truth (and does so in some sort of absolutely clear way). We like to think that revelation would be the same for everyone. We like to think that revelation would be completely consistent. This certainly fits a certain model of Biblical understanding by Evangelicals in particular, right? But, in Mormonism, the revelation is always contextual, and the best revelation is personal. If we took everyone who participates in this forum, and created a map of sorts, with all of us as dots in space, and way over there in the distance is perfect knowledge and understanding, and we drew lines to that place of perfection, we would have as many lines as we have participants. And the point of revelation is to bring us closer to that eventual goal. It isn't the point to get us to follow the same path. And so the Holy Ghost can give us personal revelation that moves us, but which doesn't necessarily look like what someone else will get. And it certainly isn't experienced in the same way or with the same understanding. This is true of ourselves as we change. The 'us' of twenty years ago (for those who are old enough for that to be meaningful) may not at all resemble the 'us' of today in many significant ways. So for us to receive even the same revelation today that we received decades ago, we might well experience it very differently and understanding it in ways that our past self simply couldn't comprehend.
Because of this conflict (the gap between what personal revelation is, and what we think it ought to be), we sometimes are presented with this idea of the untrustworthy Holy Ghost. But, I think that much of our struggle has more to do with our assumptions about revelation, and our occasional unwillingness to accept ambiguity, than it does over the accuracy of the message.
When we deal with prophets, we naturally run into a couple of challenges. The first is that we are increasingly in a different place than they were. Brigham Young is a particularly good example of this (and he has his own way of expressing these ideas that I am discussing). Unlike many of us (myself included), Brigham Young did not begin his mortality in an LDS family. He brought to his newfound religion a host of beliefs and assumptions. And the Mormonism that he knew was in many ways very different from the Mormonism that we practice today. So his lens for understanding issues (like Adam-God that is mentioned in the OP) is quite different from our own. Without that same experience, our own understanding of what Brigham Young received can be very different (even contradictory) from Brigham Young's understanding. And this shouldn't surprise us. It isn't that the revelation was wrong, or that Brigham Young received in poorly. It just was presented to him in a way that would move him from where he was to where he needed to be. Our own trajectories are very different.
So our obligation is not to be like Laman and Lemuel, but to be more like Nephi. We should receive our own revelation, not simply wait for someone else to explain it to us (through their lens of understanding). And we should be aware that the revelation (and corresponding understanding) that we receive may well be different from what others receive - but, it will be aimed at moving us in a direction appropriate for ourselves. And we should expect this difference - as an indicator that we are receiving personal revelation, and not as an indicator that the Holy Ghost is in someway untrustworthy.

Mormonism, I think, handles this issue rather well. My favorite passage of scripture which responds to this question is 2 Nephi 2. Lehi tells us that part of the purpose of mortality is to experience a limited agency - where we both act and are acted upon. This comes from the fall. And the atonement reverses aspects of the fall, leading to a post-mortal state where we experience real agency: "And because that they are redeemed from the fall they have become free forever, knowing good from evil; to act for themselves and not to be acted upon, save it be by the punishment of the law at the great and last day, according to the commandments which God hath given." (verse 26). The further explanation is that accountability only exists where we act (and not where we are acted upon). And Lehi tells us that this limited agency is sufficient for God's purposes of using mortality as a probationary state.
Because of this approach to agency (that it is limited both in scope and in consequences) in mortality, we don't actually end up with the question asked in the OP: "The trouble with the "free will" argument - god does not protect the free will of victims." The notion of a limited free will assumes exactly this. But, it also doesn't require free will in any absolute sense for everyone all the time. So it isn't exactly a "trouble". And then next: "The trouble with the "evil is educational" argument: If you want to learn something, say to learn what "love" is, who/what would be the best way to teach this lesson?" The challenge is that (at least according to Lehi), an intellectual or theoretical knowledge of Good and Evil is insufficient as a basis for absolute free will. A limited (and perhaps purely theoretical) knowledge may be sufficient within a mortal probation (depending on the circumstances). But, on some level, we all have to experience the fall that Adam and Eve experienced just so that we can come to this knowledge. God's purposes (in 2 Nephi 2), are about the end of man, and not about his creation, or even so much about this probationary state. I don't think that this creates the same sort of trouble that you mention here. I think that the sort of example you provide doesn't begin to approach the issue from that longer perspective (from a perspective external to mortality). Lehi tackles this a bit further in his discussion of opposition.
Finally: "The trouble with the "have to be tested" argument: Why are some people tested more than others? Why are some people tested beyond their limits of endurance? Why are some people sent to outer darkness by their tests, while others are given easy tests which allow them to enter the celestial kingdom?" I think that this fundamentally misunderstands the nature of the probationary state. People aren't tested beyond their limits of endurance. That doesn't meant that people aren't pushed beyond those limits in mortality - merely that at that point, it is no longer a part of the "test". Mormonism doesn't have a 'finish line' so to speak, because the test is completely individual. And the destination for one person isn't the destination for anyone else. In this way, people simply aren't sent to outer darkness.
On the other side of this coin is of course, an old debate in Mormonism over progression on the other side of mortality. I tend to side with those who believe that progression is something that happens - and that those who struggle the most in mortality simply find that they have a farther distance to go than others in their progression in the next life. As President Clark noted: "I am not a strict constructionalist, believing that we seal our eternal progress by what we do here. It is my belief that God will save all of His children that he can: and while, if we live unrighteously here, we shall not go to the other side in the same status, so to speak, as those who lived righteously; nevertheless, the unrighteous will have their chance, and in the eons of the eternities that are to follow, they, too, may climb to the destinies to which they who are righteous and serve God, have climbed to those eternities that are to come.” (J. Reuben Clark, Church News, 23 April 1960, p. 3).
What is especially significant, I think, in all of this discussion, is that our awareness of issues like rape (that you bring up) creates for us a moral and ethical obligation to be a part of the solution instead of part of the problem. We can also bring up the other great ills of our mortality - issues like displaced people and the issues that cause their situation (war, famine, prejudice). We need to keep in mind that these are all God's children, and we bear a collective responsibility to "bear one another’s burdens, that they may be light; Yea, and ... mourn with those that mourn; yea, and comfort those that stand in need of comfort, and to stand as witnesses of God at all times and in all things, and in all places that ye may be in, even until death ..."

I can't seem to post anything that is very long - I have no idea why.
In response to Kiwi earlier, here is the really short version.
I never said or implied that the Church believed that things we do not choose are sinful. What I have repeated is that the Church's view shifted from believing that same-sex attraction was itself a choice (and so sinful) to the view that it wasn't (and so stopped being sinful). That is the change.

I am not personally vested in any geographic model - so I am not all that concerned with specific interpretations of the directions. But I have a lot of reasons for not believing that Mormon and Moroni rewrote the writings of Nephi.

Polygamy is very much a regional issue. There are no polygamists that I know of in Michigan (at least in the Mormon related populations). The last Mormon related polygamy we had ended when the Strangites went away. But in my branch, we have at least three families (that I know of) with gay children. And a District President who spent a good half hour in our last District Conference going over the Church's policy towards same-sex marriage. And I don't expect that this is that unusual, where polygamy is quite unusual in the context of the larger Church.
To put it in another way, the first time I had ever seen polygamists in person, was on the family road trip last summer to the FairMormon conference. We drove to the Grand Canyon (north side) after leaving Provo, taking us through Manti, and saw a polygamist family at a gas station. Most people don't know any polygamists. They don't encounter them on a daily basis. Gay people are an entirely different group. Lots of people know someone who is gay (personally). Many people know someone who is in a same-sex relationship (or even a married gay couple). I know quite a few. I even have a nurse at my place of work that I interact with regularly who had a gender reassignment surgery a few years back. These issues are much more up front and center to most Americans than the question of polygamy - because outside of Utah, polygamy doesn't really register for us. So I don't think that the comparison sets you up to draw appropriate conclusions.

I can do that Scott.
Perhaps the best place to start is with President Kimball's Miracle of Forgiveness. He wrote:
There is this fun thing in here about how homosexuality is a result or development of earlier sins - and is a progressive behavior that starts with masturbation. (Actually, if masturbation leads to homosexuality, we ought to expect humanity to have disappeared ages ago ....). But you can see that homosexuality is defined as both "sexual desire" (same-sex attraction) and as sexual relations between same-sex individuals. This is the ambiguity where the behavior and the attraction are clearly connected, and identified as part of the same issue. Both are defined as perversions, and as sins.
This was published in 1969? So in 1984, we a memo written by Apostle Dallin H. Oaks, on August 7, 1984, titled "Principles to Govern Possible Public Statement on Legislation Affecting Rights of Homosexuals"
So Elder Oaks confirms that we had this language that was ambiguous and used for both the attraction and the sexual relations. But we also see this as part of a change to create a distinction (in the early 80s) forged by separating these earlier statements in the way that Elder Oaks does here.
However, and this is part of the reason I used this particular document, what we see here is that in the early 1980s, there is a clear view that while being an active homosexual was a grave sin, having the feelings still remains as being sinful (just not as sinful). Further, the memo later goes on in some depth to discuss issues that spring from the assumption that same-sex attraction is primarily a learned preference, and that same-sex attraction is largely a matter of choice. While the Church has been consistent in its opposition to practicing homosexuality (as sinful), these other issues have clearly changed. The Church has stopped using ambiguous language. The Church has decided that same-sex attraction is largely not a choice. And the Church has also decided that same-sex attraction is not itself sinful as was earlier believed.
It is the decision that same-sex attraction isn't a choice that really drives the changes of the last few years. Because as long as it is a choice, then the same-sex attraction is an outcome of earlier bad choices (and the jump to seeing this a sin in a chain of sins is a natural leap).
I think that any reasonable person would agree that while the Church hasn't changed its stance on homosexual relations, their view of same-sex attraction has changed quite dramatically.

If you were going to create a division for the Book of Mormon in this regard, it couldn't come at a better place internally. Why? The Book of Mormon alleges that the first two books of the Book of Mormon were written by Nephi some time in the mid 6th century B.C. The Book of Mormon alleges that the rest of the Book of Mormon was written by the father-son duo of Mormon and Moroni in the middle of the 4th century AD (a millennia later).

Let me tell you, Spencer, about my experience with this policy.
I had a gay uncle. I have brothers who have been in same sex relationships. I have a gay child.
My parents have decided to become inactive because of this policy. Several of my siblings have left the Church. And my wife told me that she no longer considers herself a Mormon. All because of this specific policy.
I think you have no place to lecture about others about how this policy has affected them. You have no clue how much pain this policy change caused for many members of the Church. You want to minimize anything that reflects negatively on the Church. Well, in my personal life, that isn't really possible in this situation.
In comparing same-sex marriage to polygamy, the policy at its core still embraces the idea that same-sex attraction is largely a matter of choice (as polygamy is). That it was implemented when Russell M. Nelson became president of the Q12 doesn't seem to me to be a coincidence. In a few years, when certain of the senior apostles have passed (and old age is something we do not recover from) and the historical animus towards those who experience same-sex attraction will diminish in the leading quorums of the Church, then the approach that the Church takes will shift again (much as happened historically with the question of blacks and the priesthood). I am absolutely certain of this.